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<table width="100%"><tr><td>pcMap(LGS)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
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<h2>A map file for Plasmodium chabaudi</h2>


<h3>Description</h3>

<p>
This is an example of a map file based on the genome of P. chabaudi. This is in part a real data as it is based on real markers. Scenarios of selection are hypothetical but realistic.
</p>


<h3>Usage</h3>

<pre>data(pcMap)</pre>


<h3>Format</h3>

<p>
A dataframe with 80 rows where each row is a marker with characteristics of map position and selection as:
</p>

<dt><code>Chr</code></dt><dd>Chromosome name. </dd>
<dt><code>Locus</code></dt><dd>Locus/marker name (a factor). </dd>
<dt><code>uCumDist</code></dt><dd>A numeric vector of user's cumulative distances (in Kosambi or Haldane cM or recombination frequency or physical distance). </dd>
<dt><code>Bins</code></dt><dd>Bins grouping markers to be tested for selection (a factor). </dd>
<dt><code>EqualFitness99</code></dt><dd>This and the remaining columns are numeric vectors represent scenarios of selection (see Details). </dd>
</p>


<h3>Details</h3>

<p>
Users should make sure that their map files contain at least the columns <code>Chr, Locus, uCumDist</code> (column names should match these names) and one or more scenario column (any name). The <code>Bins</code> column is instead optional. Additional columns are allowed and will be ignored by <code>LGS</code> functions. The order of the columns is irrelevant.
</p>
<p>
The columns of scenarios of selection specify how intensively a locus is counterselected. Each value represents the probability of an allele to be eliminated by selection and it must be between -1 and 1. Therefore, 0 means no selection (neutral marker locus). A negative or positive number is the probability that an individual carrying the 0-allele or 1-allele at that locus will be counterselected, respectively. For example, the scenario <code>EqualFitness99</code> presents only one non-neutral marker (m46 on chr. 11) and selection on this locus is set to -0.99. This means that individuals with allele '1' at this locus will survive while individuals 
with '0' have 99
</p>


<h3>Source</h3>

<p>
Katarzyna Modrzynska
</p>


<h3>References</h3>

<p>
Modrzynska et al. unpublished
</p>


<h3>Examples</h3>

<pre>
data(pcMap)
# Show map for chromosome 11 and the first two scenarios of selection
pcMap[pcMap$Chr=="11", 1:5]
</pre>



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